Workshop Description (Intermediate Course)

This workshop provides an introduction to the microbiome analyses from the raw sequence data generated from the next-generation sequencing platforms. We will cover how to perform the 16S rRNA-based analysis using an open-source bioinformatics pipeline QIIME. We will also cover some downstream analyses of the microbiome data beyond QIIME, including statistical analyses and functional analyses.

Workshop Materials

We will demonstrate the 16S rRNA gene analysis using QIIME

  1. Run QIIME on Hoffman2 or local
  2. Sequence data preparation
  3. Operational Taxonomic Units (OTU) picking, Taxonomic assignment & inferring phylogeny

Slides for day 1 can be found here.

We will demonstrate the 16S rRNA gene analysis using QIIME

  1. Microbiome diversity analyses

Slides for day 2 can be found here.

On day 3 we will learn functional analyses of the microbiome

Slides for day 3 can be found here.

Technical Requirements

  • Attendees are required to have a Hoffman2 account. To apply for an account, click here. UCLA participants who lack a faculty sponsor and non-UCLA participants may apply for a temporary Hoffman2 account, requesting sponsorship from Collaboratory Workshops.
  • We strongly encourage attendees to bring a laptop capable of accessing UCLA’s WiFi.


Michael Weinstein, Ph.D.

Guest Collaboratory Instructor
Scientist, Zymo Research



I learned a lot and was surprised that there were slides that were useful that extended analyses to other areas of metagenomics. Baochen was really patient and helpful.

I’m glad that you actually have to change some file names from the slides so people actually try to understand what the slides mean– that they are examples but you can’t just mindlessly copy and paste.

I also liked how Shin addressed things related to publications and really developed students questions.

Workshop Details

Prerequisites: None
Length: 3 days, 3 hrs per day
Level: Intermediate
Location: ZOOM
Seats Available: TBD

Fall 2020 Dates

November 17, 18, and 19

9:00 AM to 12:00 PM